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- PDB-4y6w: Crystal structure of Podosopora anserina putative kinesin light c... -

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Basic information

Entry
Database: PDB / ID: 4y6w
TitleCrystal structure of Podosopora anserina putative kinesin light chain nearly identical TPR-like repeats
ComponentsNaB(AB)3ACb - light chain TPR-like repeats
KeywordsUNKNOWN FUNCTION / Tetratricopeptide repeat / 42PR / TPR
Function / homology
Function and homology information


NB-ARC / NB-ARC domain / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.587 Å
AuthorsMarold, J.D. / Kavran, J.M. / Bowman, G.D. / Barrick, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM068462 United States
CitationJournal: Structure / Year: 2015
Title: A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins.
Authors: Marold, J.D. / Kavran, J.M. / Bowman, G.D. / Barrick, D.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NaB(AB)3ACb - light chain TPR-like repeats


Theoretical massNumber of molelcules
Total (without water)25,8271
Polymers25,8271
Non-polymers00
Water2,072115
1
A: NaB(AB)3ACb - light chain TPR-like repeats

A: NaB(AB)3ACb - light chain TPR-like repeats


Theoretical massNumber of molelcules
Total (without water)51,6542
Polymers51,6542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4090 Å2
ΔGint1 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.071, 92.341, 30.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NaB(AB)3ACb - light chain TPR-like repeats


Mass: 25826.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Strain: S mat+ / Gene: CDP31375.1 / Plasmid: pET15b / Cell line (production host): ROSETTA 2 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: A0A090CRQ5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295.16 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, 30% PEG 4000, 5mM TCEP

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0375 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: ...Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0375 Å / Relative weight: 1
ReflectionResolution: 1.587→40.12 Å / Num. obs: 32123 / % possible obs: 99.68 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.114 / Rsym value: 0.112 / Net I/σ(I): 18.6
Reflection shellResolution: 1.587→1.643 Å / Redundancy: 14 % / Mean I/σ(I) obs: 7 / % possible all: 98.14

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y6C

4y6c


Resolution: 1.587→40.12 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 2000 6.23 %Random selection
Rwork0.1778 ---
obs0.1794 32122 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.587→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 115 1790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051701
X-RAY DIFFRACTIONf_angle_d0.9512298
X-RAY DIFFRACTIONf_dihedral_angle_d17.685662
X-RAY DIFFRACTIONf_chiral_restr0.038258
X-RAY DIFFRACTIONf_plane_restr0.004314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5866-1.62630.22651380.17832074X-RAY DIFFRACTION97
1.6263-1.67020.21911400.18162107X-RAY DIFFRACTION100
1.6702-1.71940.21291410.17892123X-RAY DIFFRACTION100
1.7194-1.77490.22151400.17822123X-RAY DIFFRACTION100
1.7749-1.83830.21791420.17992128X-RAY DIFFRACTION100
1.8383-1.91190.21811420.18252138X-RAY DIFFRACTION100
1.9119-1.99890.22641400.17882111X-RAY DIFFRACTION100
1.9989-2.10430.2091420.16862150X-RAY DIFFRACTION100
2.1043-2.23610.17141430.16352146X-RAY DIFFRACTION100
2.2361-2.40880.1911440.16462167X-RAY DIFFRACTION100
2.4088-2.65110.19661430.17212153X-RAY DIFFRACTION100
2.6511-3.03460.20251450.19072186X-RAY DIFFRACTION100
3.0346-3.82290.21281470.17782228X-RAY DIFFRACTION100
3.8229-40.13320.20131530.18362288X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -10.3888 Å / Origin y: 5.8902 Å / Origin z: -0.4572 Å
111213212223313233
T0.1144 Å20.0165 Å20.0162 Å2-0.1321 Å2-0.005 Å2--0.1065 Å2
L0.6175 °20.1476 °20.019 °2-1.8084 °2-0.1671 °2--0.3355 °2
S0.0577 Å °0.0313 Å °0.005 Å °0.0234 Å °-0.0443 Å °-0.1212 Å °-0.0223 Å °-0.0192 Å °-0.0114 Å °
Refinement TLS groupSelection details: all

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